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<div class="title">C:/Users/cmbruns/svn/moltk/c++/include/moltk/Alignment.h</div>  </div>
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<a href="Alignment_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00020"></a>00020 <span class="comment">*/</span>
<a name="l00021"></a>00021 
<a name="l00022"></a>00022 <span class="preprocessor">#ifndef MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00023"></a>00023 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span>
<a name="l00025"></a>00025 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &quot;<a class="code" href="Printable_8h.html">moltk/Printable.h</a>&quot;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &quot;<a class="code" href="Biosequence_8h.html">moltk/Biosequence.h</a>&quot;</span>
<a name="l00030"></a>00030 
<a name="l00031"></a>00031 <span class="keyword">namespace </span>moltk {
<a name="l00032"></a>00032 
<a name="l00033"></a><a class="code" href="classmoltk_1_1Alignment.html">00033</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment.html">Alignment</a> : <span class="keyword">public</span> std::vector&lt; std::string &gt; , <span class="keyword">public</span> moltk::<a class="code" href="classmoltk_1_1Printable.html" title="moltk::Printable is an abstract base class to help streamline string conversion in the moltk python b...">Printable</a>
<a name="l00034"></a>00034 {
<a name="l00035"></a>00035 <span class="keyword">public</span>:
<a name="l00036"></a><a class="code" href="classmoltk_1_1Alignment_1_1Column.html">00036</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment_1_1Column.html">Column</a>
<a name="l00037"></a>00037     {
<a name="l00038"></a>00038     };
<a name="l00039"></a>00039 
<a name="l00040"></a>00040 <span class="keyword">public</span>:
<a name="l00041"></a>00041     <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>();
<a name="l00042"></a>00042     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html">Biosequence</a>&amp;);
<a name="l00043"></a>00043     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> std::string&amp;);
<a name="l00044"></a>00044     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>*);
<a name="l00045"></a>00045     
<a name="l00046"></a>00046     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment_1_1Column.html">Column</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a47ff0fe2dfbf84eaf79dd829983e42f5">column</a>(<span class="keywordtype">size_t</span> ix) <span class="keyword">const</span>;
<a name="l00047"></a>00047     <a class="code" href="classmoltk_1_1Alignment_1_1Column.html">Column</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a47ff0fe2dfbf84eaf79dd829983e42f5">column</a>(<span class="keywordtype">size_t</span> ix);
<a name="l00048"></a>00048 
<a name="l00049"></a>00049     <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a2e94d39fcbad3289fa8d3105784e3da6">print_to_stream</a>(std::ostream&amp; os) <span class="keyword">const</span>;
<a name="l00050"></a>00050 };
<a name="l00051"></a>00051 
<a name="l00052"></a>00052 <span class="comment">// std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, const moltk::Alignment&amp; p);</span>
<a name="l00053"></a>00053 
<a name="l00054"></a>00054 } <span class="comment">// namespace moltk</span>
<a name="l00055"></a>00055 
<a name="l00056"></a>00056 
<a name="l00057"></a>00057 <span class="preprocessor">#endif // MOLTK_ALIGN_ALIGNMENT_H</span>
</pre></div></div>
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